Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019040.1 Corchorus olitorius cultivar O-4 contig19073, whole genome shotgun sequence

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 7800
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30


Found at i:4766 original size:10 final size:10

Alignment explanation


    Indices: 4747--4786  Score: 62
    Period size: 10  Copynumber: 4.0  Consensus size: 10

       4737 GGATTGGTCC

                 *    
       4747 TTCCCTTCCT
          1 TTCCCCTCCT

                      
       4757 TTCCCCTCCT
          1 TTCCCCTCCT

                      
       4767 TTCCCCTCCT
          1 TTCCCCTCCT

                 *    
       4777 TTCCCATCCT
          1 TTCCCCTCCT

       4787 ATCCTGTCCT


Statistics
Matches: 28,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  10   28  1.00

ACGTcount: A:0.03, C:0.55, G:0.00, T:0.42


Consensus pattern (10 bp):   
TTCCCCTCCT

Found at i:4798 original size:20 final size:20

Alignment explanation


    Indices: 4744--4790  Score: 60
    Period size: 20  Copynumber: 2.4  Consensus size: 20

       4734 CAAGGATTGG

                     *         *
       4744 TCCT-TCCCTTCCTTTCCCC
          1 TCCTATCCCCTCCTTTCCCA

                *               
       4763 TCCTTTCCCCTCCTTTCCCA
          1 TCCTATCCCCTCCTTTCCCA

                    
       4783 TCCTATCC
          1 TCCTATCC

       4791 TGTCCTTTAC


Statistics
Matches: 24,  Mismatches: 3, Indels: 1
        0.86            0.11        0.04

Matches are distributed among these distances:
  19    4  0.17
  20   20  0.83

ACGTcount: A:0.04, C:0.55, G:0.00, T:0.40


Consensus pattern (20 bp):   
TCCTATCCCCTCCTTTCCCA

Found at i:6851 original size:51 final size:51

Alignment explanation


    Indices: 6777--6883  Score: 137
    Period size: 51  Copynumber: 2.1  Consensus size: 51

       6767 GTTCTTCATA

                                            **         *       
       6777 TTTT-TCTTGTTTAGATCTTGTCTCAGGACATTCAAACACTCTTTTAGTGT
          1 TTTTCTCTTGTTTAGATCTTGTCTCAGGACATAAAAACACTCTATTAGTGT

                                      *               *    *    
       6827 TTTTCTCTTGTTTCA-ATCTTGTCTCCGGACATAAAAACACTGTATTCGTGT
          1 TTTTCTCTTGTTT-AGATCTTGTCTCAGGACATAAAAACACTCTATTAGTGT

                  
       6878 TTTTCT
          1 TTTTCT

       6884 TTCAGAAATA


Statistics
Matches: 49,  Mismatches: 6, Indels: 3
        0.84            0.10        0.05

Matches are distributed among these distances:
  50    4  0.08
  51   44  0.90
  52    1  0.02

ACGTcount: A:0.20, C:0.20, G:0.13, T:0.48


Consensus pattern (51 bp):   
TTTTCTCTTGTTTAGATCTTGTCTCAGGACATAAAAACACTCTATTAGTGT
Done.